Paulo Miki was born into a rich family. He was educated by Jesuits in Azuchi and Takatsuki. He joined the Society of Jesus and preached the gospel for his fellow citizens. The Japanese government feared the Jesuit's influences and persecuted them. Miki was jailed, along with others. He and his Catholic peers were forced to walk 600 miles (≈966 kilometers) from Kyoto while singing the Te Deum as a punishment for the community. Finally they arrived at Nagasaki, the city which had the most conversions to Christianity, and Miki was crucified on 5 February 1597. He preached his last sermon from the cross, and it is maintained that he forgave his executioners, stating that he himself was Japanese. Alongside him died Joan Soan (de Gotó) and Santiago Kisai, of the Society of Jesus, in addition to twenty-three clergy and laity, all of whom were canonized by Pope Pius IX in 1862.

The other memorial, which was presented to the Pope in March, 1598, said that it was not hatred of Christianity but fear of the excessive power of the Jesuits that led Hideyoshi to oppose their teaching ; that the Jesuits alone were proscribed, while the Franciscans had been treated with honor and given liberty to preach the Gospel, which they did with so much success as to lead back many that had apostatized ; and that Valegnani when in Japan had appeared in court with an equipage not becoming a priest, for he wore pontifical garments, had a miter on his head, and was followed by two hundred men in livery.
The Jesuits, aware of these attacks, took means for defending themselves ; but ere either the charges or the defense could have reached Europe, both Jesuits and Franciscans were feeling the force of Hideyoshi’s wrath. No sooner had the Taiko been informed of what the Spanish pilot had said than he took action. On the evening of December 9, 1596, th establishments of the Franciscans and Jesuits in Kyoto and Osaka were surrounded by guards. The governors of the two cities were ordered to draw up lists of persons who were in the habit of frequenting the churches. In a few days three Franciscan Fathers (Baptiste, Aguirre, and Blanco), three Franciscan Brothers (Las Casa, Parilha, and Garcia), Paul Miki, who was a lay brother of the Society of Jesus, two other Japanese who were novices preparing to enter the same Society, and fifteen persons in the employ of the missionaries were arrested.
On the third of January, 1597, the twenty-four prisoners were led through the streets of Kyoto to the northern part of the city, where the executioner cut off portions of their ears. They were put on carts, three in each cart, and drawn through the city in order to expose them to the derision of the populace. Before each cart was suspended a placard which said in substance : “The Taiko has condemned these men to die because, though coming from the Philippine Islands as ambassadors, they have disobeyed commands by preaching the Christian religion. Therefore, they and the Japanese that have become their followers shall be crucified in Nagasaki.”

Ashikaga Yoshiteru (足利 義輝?, March 31, 1536—June 17, 1565), also known as Yoshifushi of Yoshifuji, was the 13th shogun of the Ashikaga shogunate who reigned from 1546 to 1565 during the late Muromachi period of Japan. He was the eldest son of the 12th shogun, Ashikaga Yoshiharu; and his mother was a daughter of Konoe Taneie (later called 慶寿院 Keijuin). When he became shogun in 1546 at age 11, Yoshiteru's name was Yoshifushi (sometimes translated as Yoshifuji); but some years later in 1554, he changed his name to the one by which he is conventionally known today. His younger brother Ashikaga Yoshiaki would become the fifteenth shogun."

The next day they were put on pack-horses and sent to Osaka. They were led through the principle streets of that city and Sakai, after which they were taken by land to Nagasaki. Everywhere they were subjected to the insults of the people, although in some places through which they passed the Christians came to speak words of cheer and exhorted them to be faithful unto death. By this protracted journey, which took over two months, a large part of the country was warned of the danger of following the foreign religion, while the place of execution was evidently chosen with the thought of having the Portuguese report to the people of Christian lands that missionaries could come to Japan only at peril of their lives.
As a boy, Hasaburo had been a playmate of Paul Miki, and for years he had seen nothing of him until he met him among the captives that he must put to death.
There were fears that the Christians of Nagasaki might seek to rescue their fellow-believers. The prisoners were not brought into the city until the day (February 5, 1597) that they were to die, and then, instead of being taken to the usual execution-ground, they were led to a hill whose approaches could be easily guarded by men with muskets and spears. Death was by crucifixion, a method of punishment said to have been unknown among the Japanese until they heard of it in connection with Christianity. It afterward became a common form of executing those guilty of heinous crimes. As it was practiced by the Japanese, the victims was tied by ropes to a cross and , instead of being led to suffer for a long time, his body was pierced with a spear that was first thrust from the right side upwards towards the left shoulder and then from the left side towards the right shoulder. Thus the heart was usually pierced, causing instant death It may be that this use of the spear was borrowed from representations that had been seen of the crucifixion of Christ.
After the martyrs had been bound to the crosses, some of them, especially Paul Miki, addressed the crowd of Christians and others who were pressing up as near as possible to them. Fathers Paez and Rodriguez had obtained permission to remain with the sufferers. Two Franciscans in disguise were in the crowd that stood outside the cordon of soldiers. When at last the execution was over, the Christians, unmindful of the blows that the guards bestowed upon them, pressed forwards through the lines to dip kerchiefs in the blood of the martyrs or to obtain shreds of their clothing.
In after times various stories were told of bright lights that shone over the martyrs, of the bodies that did not suffer corruption in the two months that they were left on the crosses, of blood that remained in a liquid state, and of a dumb woman who received the power of speech when she kissed Father Baptiste’s cross. Two witnesses declared that ere the bodies were removed they saw Father Baptiste celebrating mass in the church, assisted by one of the martyred children. Amazed at this, they went to the execution-ground where the cross of the Father seemed to be empty. The guards told them that the body often vanished and after a short absence returned to its place. These and other alleged marvels constituted a part of what was considered essential for justifying the canonization of those who are now known as the Twenty-Six Martyrs, for it was not long ere steps were taken towards having them enrolled among the saints of the Roman Catholic Church. A brief issued September 14, 1627, by Pope Urban VIII authorized the Franciscans to say the office and mass of the six priests and seventeen laymen connected with their order, and another issued the next day gave permission for the Jesuits to honor their martyrs in the same way. The canonization to which this beatification formed a necessary prelude was long delayed ; the chief reason, it is said, being the great expense involved. In March, 1862, Pius IX pronounced the decree of canonization, the imposing ceremonies connected therewith being performed the next June.
Rumors that Hideyoshi was soon coming to Kyushu made the officials think it wise to enforce the edicts against the Christians. Early in 1598, one hundred and thirty-seven churches, the college in Amakusa, the seminary in Arima, and many residences of the Jesuits were destroyed. In some places the Christians were subjected to severe persecution. Those missionaries that did not succeed in concealing themselves were brought to Nagasaki for deportation.

Tempera painting of the martyr of Saint Sebastian, 1590-1600, Japan.

The Japanese government used Fumie to reveal practicing Catholics and sympathizers. Fumie were pictures of the Virgin Mary and Christ. Government officials made everybody trample on these pictures. People reluctant to step on the pictures were identified as Catholics and then sent to Nagasaki. The policy of the Japanese government (Edo) was to turn them from their faith. If the Catholics refused to change their religion, they were tortured. Many of them still refusing to abandon their faith were executed on Nagasaki's Mount Unzen.

Bishop Martinez died in 1598 while on his way to India, and in August of the same year his successor, Mgr. Cerqueira, arrived in Japan. One of the first acts of the new bishop was to call together the leading missionaries for a consultation upon the question of slaves. The Portuguese merchants had been in the habit of purchasing prisoners of war and criminals, who were sold by the feudal lords, sometimes as slaves, sometimes as servants for a limited number of years. Bishop Martinez at first had issued licenses for this trade, but had afterward prohibited it under pain of a fine, major excommunication, and the loss of the slaves thus bought. The new Bishop now asked advice as to the policy that he should pursue. The conference was unanimous in its opinion that he ought to renew the prohibition made by his predecessor, and to abstain scrupulously from giving any of the Portuguese licenses to buy or take away from Japan persons purchased either as slaves or under the name of servants bound for a certain number of years. He ought also to urge the King of Spain to renew and enforce laws concerning the liberty of the Japanese that had formerly been published by King Sebastian of Portugal. The report of this conference shows that the trade had been attended to terrible evils.
It was feared that Hideyoshi would be aroused to renewed activity against Christianity by an incident that happened about this time. Among the Franciscans that had escaped arrest in 1596, was one named Jerome de Jesus. Great efforts had been made to find him. According to one account, he was finally apprehended and sent to Manila ; others say he had gone there of his own accord. However this may have been in June 1598, he, with another of his order, took passage from the Philippines in a Japanese vessel, whose crew betrayed them to the officials fo Nagasaki. The Franciscans were arrested, but Jerome’s knowledge of the country enabled him to escape. The Vice-Provincial of the Jesuits sent a messenger to Terasawa begging him not to have this reported to Hideyoshi. Terasawa accordingly sent his officers orders to keep the affair secret, but to put forth every effort for recapturing the fugitive. Enemies of the Jesuits hint that the latter had a part in securing the original arrest of the Franciscans and would have been glad to hear that Jerome had been again apprehended.
Immediate danger of increased persecution was removed by the death of Hideyoshi on September 16, 1598. He was undoubtedly one of the shrewdest statesmen Japan has ever produced. A recent writer goes so far as to call him “the greatest man Japan has every seen,” and also, “the greatest statesman of the century, whether in Japan or in Europe.” Whatever his talents, there was much clay mingled with the iron ; and it is not a cause for wonder that in the letters of the missionaries and in the histories founded upon them much emphasis is laid on the weak points in his character. In ecclesiastical history he will be remembered as a persecutor, and yet it should not be forgotten that throughout most of the time that he was in authority the teachers of a foreign religion were left unmolested, that he held some of them, as Organtin and Rodriguez, in high esteem, and that he appointed to important offices those that were recognized as leaders among the Christians. It is not strange that, seeing the splendor of some of the religious ceremonies and the honor shown by the believers to their teachers, he feared lest Christianity would succeed to the political and even to the military powers that had been held by some of the Buddhist sects ere they had been crushed by Nobunaga and himself.

We may at first by inclined to smile at the suspicions aroused by the unfortunate remarks of the Spanish pilot ; yet the mere fact that within a hundred years the Spanish kings had gained possession of much of American and India as well as of the Philippines and other islands, might well give cause for apprehension. Hideyoshi knew that messengers had been sent by the Christian daimyos of Kyushu to greet the King of Spain, and to bow at the feet of the Pope. Had he been acquainted with what European rulers and the Popes had done in connection with new countries, his fears would not have been lessened. Pope Martin V about 1418, had granted to the King of Portugal all the territories that might be discovered by his navigators between Cape Bodajor and India. This grant was afterward confirmed by Eugene IV. Similar concessions were made to the Spaniards for any discoveries they might make in sailing westward. In 1479 the rulers of Spain and Portugal had agreed that each would respect what had been granted to the other by these papal decrees. In 1493 Pope Alexander VI issued his famous Bull of Demarcation, authorizing Spain, on condition of planting the Catholic Church to take possession of all lands that lie beyond the meridian drawn one hundred leagues west of the Azores, so far as these lands were not already subject to Christian powers. Though Portugal was not mentioned, it was understood that she could have all lying east of that meridian. Of Cabral, who was sent out from Portugal towards India in 1500, it has been said : “The sum of his instructions was to begin with preaching, and, if that failed to proceed to the sharp determination of the sword.”
The history of Spain at that time abounds with examples of this vicious linking together of religion and the power of the sword. The civil and ecclesiastical counselors drew up a form of proclamation to be used by the invaders of new provinces in America. In case the rulers and people hesitated to acknowledge allegiance to Spain and to the Church, the invader was to give this warning : “If you refuse ; by the help of God we shall enter with force into your land, and shall make war against you in all ways and manners that we can, and subject you to the yoke and obedience of the Church and of their Highness ; we shall take you and your wives and your children and make slaves of them, and sell and dispose of them as their Highness may command ; and we shall take away your goods, and do you all the mischief and damage that we can, as to vassals who do not obey and refuse to receive their lord ; and we protest that the deaths and losses that shall accrue from this are your own fault.”

Hasekura Tsunenaga converted to Catholicism in Madrid in 1615.

Another proof that Hideyoshi’s fears were not altogether foolish may be found in the fact that in 1575, twenty years before the ambassadors came to Japan from the Philippines, Captain Maldonado had sent from the same islands a report in which he asked that five hundred soldiers be sent from Spain in order that he might attempt the conquest of Loochoo and Japan.
The remembrance that Philip II of Spain died only three days before Hideyoshi, may suggest a comparison between the two men and lead us to ask what would havbe happened if conditions had been reversed so that Japanese teachers of Buddhism had attempted to carry their religion to Spain and had pursued the methods that were sued by the Jesuit and Franciscan missionaries. One man’s errors do not excuse those of another ; but a comparison of Hideyoshi and Philip may at least help to soften our condemnation of the former, who, whatever his faults, does no deserve to have his name places high in the list of those who in the sixteenth century were noted for religious intolerance.